[BioC] limma and paired data

[Danielle Fletcher]

Hi,
 
I am using limma to analyse a 2-colour microarray experiment. There are 2 treatments and 4 replicates in each of these groups. Each replicate is paired to a replicate in the otehr treatment group. Each sample was hybridised with a reference, so 8 slides in total.
 
The targets file looks like this (hopefuly that will make it clearer):
SlideNumber   Name   FileName   Cy3   Cy5
1   1M   1.gpr   monolayer   ref
2   1P   5b.gpr   pellet   ref
3   2M   2.gpr   monolayer   ref
4   2P   7.gpr   pellet   ref
5   3M   3.gpr   monolayer   ref
6   3P   6.gpr   pellet   ref
7   4M   B.gpr   monolayer   ref
8   4P   A.gpr   pellet   ref
 
Initially my design matrix looked like this:
 
   Sample-Ref Monolayer-Pellet
1M           1          0
1P           1          1
2M           1          0
2P           1          1
3M           1          0
3P           1          1
4M           1          0
4P           1          1
 
but thinking about it again, i don't think this takes into account the paired nature of the data. I am sure that the answer is probably a simple one, but I am not sure what the best solution is.  I would appreciate any advice.
 
Thanks in advance
 
Danielle


		
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